RetrogeneDB ID: retro_ogar_2360

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873615.1:3054409..3055518(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSOGAG00000005352
• Aliases: None
• Description: pre-mRNA processing factor 3 [Source:HGNC Symbol;Acc:17348]

Sequence

>retro_ogar_2360
ATGGCACTTTCTAAGAGGGAGCTGGATGAGCTGAAACAATGGATAGAGAAGACAGTAAGGTGAGTACTGGGTTTCTCAGA
GCCCACAGTGGTAACAGCAGCACTGAACTGTGTGGGGAAGGGCATGGACAAGAAGAGGACAGCCGACCATCTGAAACCTT
TTCTTGATGATTCTACTCTCTGATTTGTGGACAAACTATTTGAGGCTGTGGAGGAGGGCTGGAGCTGTAGGCATTCCAAG
TCTAGTAGTGATAGGAGCAAAAAATGAGAGCTAAAGGAGGTGTTTGATGATGACTCTGAGATTTCCAAAGAATCTTTGGG
AGTAAAGAAGCGATGAATACCCCATTTTGAGGAAGCGGAAGAAGAGCCAGAGGTGATCCCTAGTCCTCCATCAGAGAGCC
TGGGCATGCTGACTAAGCTCCAGATCAATGGAGCAGCAATATGACAAATTGAGGAGAGAAAAAAACAACTGAGCTTCATT
AGTCTCCCTACACCTCAGCCAAAGACTCCTTCTTCCCCCTAACCAGAGAGACCTCCAATTGGCAACACTATTCAGCCCTC
CCAGGCTGCCACTTTCATGAATGATGCCATTGAGAAAGCAAGGAAAGCAGCTGAACTACAAGCTCGAATCCAAGCCCAGC
GGTTCCTGAAGCCAGGACTCATTGGCAATGCCAACATGGTGGGCTTGGCTAATCTCCATGCTATGGACATTGCTCCCCTG
AAGGTGGAGTTAAAAGATCAAACGAAACCTACACCACTGATCCTAGATGAACAGGGTGACACTGTAGATGCAACAGGCAA
GGAAACTGAGCTGACACATCCATGCCTACTCTTAAGGCCAATATTCGTTCTGTGAAAAGGGAACAATTCAAGCAACGGCT
AAAAGAAAAGCCATCAGAAGATATGGAGTCCAATACATTTTTTGACCCCTGAGTTTCAACTGCCCCTTCCCAACGTCAGA
GATGAATTTTTAAATTCCATGACAGAGGCAAATTTGAGAAGATTGAACAGCGATTACAGACCAAGGCTCAACTGGACAAG
CAGCAGGCAGAGATCTCACAGGCAGCTTGAAAAACAGGCATCCATACTTCCACTAGGCTTGCCCTCATT

Alignment

ORF - retro_ogar_2360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 54.69 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAV
          MALSKRELDELK.WIEKTV..VLGFSEPTVVTAALNCVGKGMDKK..ADHLKPFLDDSTL.FVDKLFEAV
Retrocopy MALSKRELDELKQWIEKTVR*VLGFSEPTVVTAALNCVGKGMDKKRTADHLKPFLDDSTL*FVDKLFEAV

Parental  EEGRSSRHSKSSSDRSRKRELKEVFGDDSEIAKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKL
          EEG.S.RHSKSSSDRS.K.ELKEVF.DDSEI.KES.GVKKR.IP.FEE.EEEPEVIP.PPSES.GMLTKL
Retrocopy EEGWSCRHSKSSSDRSKK*ELKEVFDDDSEISKESLGVKKR*IPHFEEAEEEPEVIPSPPSESLGMLTKL

Parental  QIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQ
          QI.....AA..QIEERKKQLSFIS.PTPQPKTPSS..PER.PIGNTIQPSQAATFMNDAIEKARKAAELQ
Retrocopy QIN---GAAI*QIEERKKQLSFISLPTPQPKTPSSP*PERPPIGNTIQPSQAATFMNDAIEKARKAAELQ

Parental  ARIQAQLALKPGLIGNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTH-RMP
          ARIQAQ..LKPGLIGNANMVGLANLHAM.IAP.KVELKDQTKPTPLILDEQG.TVDATGKE.ELTH..MP
Retrocopy ARIQAQRFLKPGLIGNANMVGLANLHAMDIAPLKVELKDQTKPTPLILDEQGDTVDATGKETELTH<SMP

Parental  TLKANIRAVKREQFKQQLKEKPSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAHNH
          TLKANIR.VKREQFKQ.LKEKPSEDMESNTFFDP.VS.APSQRQR..FKFHD.GKFEKI.QRL.TKA...
Retrocopy TLKANIRSVKREQFKQRLKEKPSEDMESNTFFDP*VSTAPSQRQR*IFKFHDRGKFEKIEQRLQTKAQLD

Parental  KMEAELAQASRDGAIHPGTYWYLI
          K..AE..QA.....IH..T...LI
Retrocopy KQQAEISQAA*KTGIHTSTRLALI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2360 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009926	1 retrocopy	retro_cjac_1499,
Macaca mulatta	ENSMMUG00000016301	1 retrocopy	retro_mmul_2348,
Nomascus leucogenys	ENSNLEG00000009841	1 retrocopy	retro_nleu_2529,
Otolemur garnettii	ENSOGAG00000005352	4 retrocopies	retro_ogar_2360 , retro_ogar_3052, retro_ogar_374, retro_ogar_409,
Pan troglodytes	ENSPTRG00000001254	1 retrocopy	retro_ptro_2758,